Integrated genetic analysis systems

The overall objective of this thesis is to integrate a number of micro/nanotechnologies into integrated cartridge type systems to implement such biochemical protocols. Instrumentation and systems were developed to interface such cartridge systems: (i) implementing microfluidic handling, (ii) executing thermal control during biochemical protocols and (iii) detection of biomolecules associated with inherited or infectious disease. This system implements biochemical protocols for DNA extraction, amplification and detection. A digital microfluidic chip (ElectroWetting on Dielectric) manipulated droplets of sample and reagent implementing sample preparation protocols. The cartridge system also integrated a planar magnetic microcoil device to generate local magnetic field gradients, manipulating magnetic beads. For hybridisation detection a fluorescence microarray, screening for mutations associated with CFTR gene is printed on a waveguide surface and integrated within the cartridge. A second cartridge system was developed to implement amplification and detection screening for DNA associated with disease-causing pathogens e.g. Escherichia coli. This system incorporates (i) elastomeric pinch valves isolating liquids during biochemical protocols and (ii) a silver nanoparticle microarray for fluorescent signal enhancement, using localized surface plasmon resonance. The microfluidic structures facilitated the sample and reagent to be loaded and moved between chambers with external heaters implementing thermal steps for nucleic acid amplification and detection. In a technique allowing probe DNA to be immobilised within a microfluidic system using (3D) hydrogel structures a prepolymer solution containing probe DNA was formulated and introduced into the microfluidic channel. Photo-polymerisation was undertaken forming 3D hydrogel structures attached to the microfluidic channel surface. The prepolymer material, poly-ethyleneglycol (PEG), was used to form hydrogel structures containing probe DNA. This hydrogel formulation process was fast compared to conventional biomolecule immobilization techniques and was also biocompatible with the immobilised biomolecules, as verified by on-chip hybridisation assays. This process allowed control over hydrogel height growth at the micron scale.

A novel CE microchip with micro pillars column & double-L injection design for Capacitance Coupled Contactless Conductivity detection technology

This novel capillary electrophoresis microchip, or also known as μTAS (micro total analysis system) was designed to separate complex aqueous based compounds, similar to commercial CE & microchip (capillary electrophoresis) systems, but more compact. This system can be potentially used for mobile/portable chemical analysis equipment. Un-doped silicon wafer & ultra-thin borofloat glass (Pyrex) wafers have been used to fabricate the device. Double-L injection feature, micro pillars column, bypass separation channel & hybrid- referenced C4D electrodes were designed to achieve a high SNR (signal to noise ratio), easy- separation, for a durable and reusable μTAS for CE use.

Average-case analysis of power consumption in embedded systems

Power efficiency is one of the most important constraints in the design of embedded systems since such systems are generally driven by batteries with limited energy budget or restricted power supply. In every embedded system, there are one or more processor cores to run the software and interact with the other hardware components of the system. The power consumption of the processor core(s) has an important impact on the total power dissipated in the system. Hence, the processor power optimization is crucial in satisfying the power consumption constraints, and developing low-power embedded systems. A key aspect of research in processor power optimization and management is “power estimation”. Having a fast and accurate method for processor power estimation at design time helps the designer to explore a large space of design possibilities, to make the optimal choices for developing a power efficient processor. Likewise, understanding the processor power dissipation behaviour of a specific software/application is the key for choosing appropriate algorithms in order to write power efficient software. Simulation-based methods for measuring the processor power achieve very high accuracy, but are available only late in the design process, and are often quite slow. Therefore, the need has arisen for faster, higher-level power prediction methods that allow the system designer to explore many alternatives for developing powerefficient hardware and software. The aim of this thesis is to present fast and high-level power models for the prediction of processor power consumption. Power predictability in this work is achieved in two ways: first, using a design method to develop power predictable circuits; second, analysing the power of the functions in the code which repeat during execution, then building the power model based on average number of repetitions. In the first case, a design method called Asynchronous Charge Sharing Logic (ACSL) is used to implement the Arithmetic Logic Unit (ALU) for the 8051 microcontroller. The ACSL circuits are power predictable due to the independency of their power consumption to the input data. Based on this property, a fast prediction method is presented to estimate the power of ALU by analysing the software program, and extracting the number of ALU-related instructions. This method achieves less than 1% error in power estimation and more than 100 times speedup in comparison to conventional simulation-based methods. In the second case, an average-case processor energy model is developed for the Insertion sort algorithm based on the number of comparisons that take place in the execution of the algorithm. The average number of comparisons is calculated using a high level methodology called MOdular Quantitative Analysis (MOQA). The parameters of the energy model are measured for the LEON3 processor core, but the model is general and can be used for any processor. The model has been validated through the power measurement experiments, and offers high accuracy and orders of magnitude speedup over the simulation-based method.

Analysis of institutional arrangements and common pool resources governance: the case of Lake Tana sub-basin, Ethiopia

Although Common Pool Resources (CPRs) make up a significant share of total income for rural households in Ethiopia and elsewhere in developing world, limited access to these resources and environmental degradation threaten local livelihoods. As a result, the issues of management, governance of CPRs and how to prevent their over-exploitation are of great importance for development policy. This study examines the current state and dynamics of CPRs and overall resource governance system of the Lake Tana sub-basin. This research employed the modified form of Institutional Analysis and Development (IAD) framework. The framework integrates the concept of Socio-Ecological Systems (SES) and Interactive Governance (IG) perspectives where social actors, institutions, the politico-economic context, discourses and ecological features across governance and government levels were considered. It has been observed that overexploitation, degradation and encroachment of CPRs have increased dramatically and this threatens the sustainability of Lake Tana ecosystem. The stakeholder analysis result reveals that there are multiple stakeholders with diverse interest in and power over CPRs. The analysis of institutional arrangements reveals that the existing formal rules and regulations governing access to and control over CPRs could not be implemented and were not effective to legally bind and govern CPR user’s behavior at the operational level. The study also shows that a top-down and non-participatory policy formulation, law and decision making process overlooks the local contexts (local knowledge and informal institutions). The outcomes of examining the participation of local resource users, as an alternative to a centralized, command-and-control, and hierarchical approach to resource management and governance, have called for a fundamental shift in CPR use, management and governance to facilitate the participation of stakeholders in decision making. Therefore, establishing a multi-level stakeholder governance system as an institutional structure and process is necessary to sustain stakeholder participation in decision-making regarding CPR use, management and governance.

Physico-chemical properties and component interactions in high solids food systems

The present study aimed to investigate interactions of components in the high solids systems during storage. The systems included (i) lactose–maltodextrin (MD) with various dextrose equivalents at different mixing ratios, (ii) whey protein isolate (WPI)–oil [olive oil (OO) or sunflower oil (SO)] at 75:25 ratio, and (iii) WPI–oil– {glucose (G)–fructose (F) 1:1 syrup [70% (w/w) total solids]} at a component ratio of 45:15:40. Crystallization of lactose was delayed and increasingly inhibited with increasing MD contents and higher DE values (small molecular size or low molecular weight), although all systems showed similar glass transition temperatures at each aw. The water sorption isotherms of non-crystalline lactose and lactose–MD (0.11 to 0.76 aw) could be derived from the sum of sorbed water contents of individual amorphous components. The GAB equation was fitted to data of all non-crystalline systems. The protein–oil and protein–oil–sugar materials showed maximum protein oxidation and disulfide bonding at 2 weeks of storage at 20 and 40°C. The WPI–OO showed denaturation and preaggregation of proteins during storage at both temperatures. The presence of G–F in WPI–oil increased Tonset and Tpeak of protein aggregation, and oxidative damage of the protein during storage, especially in systems with a higher level of unsaturated fatty acids. Lipid oxidation and glycation products in the systems containing sugar promoted oxidation of proteins, increased changes in protein conformation and aggregation of proteins, and resulted in insolubility of solids or increased hydrophobicity concomitantly with hardening of structure, covalent crosslinking of proteins, and formation of stable polymerized solids, especially after storage at 40°C. We found protein hydration transitions preceding denaturation transitions in all high protein systems and also the glass transition of confined water in protein systems using dynamic mechanical analysis.